Exploring the gut microbiome of sympatric closely related fish through next generation sequencing

Type:

Internship position (12 ECTS)

programme:

EMBC+

Oceans and Lakes

Microorganisms in the digestive tract of animals can influence the health, physiology and behaviour of the host. Gut symbionts can supplement the host genome with functional genes that can extent the host niche (for example through the exploitation of nutrients that cannot be exploited by the host genome) and can provide opportunities to adapt to new environmental conditions. In turn, the host genome can alter the gut microbiome. Recent studies in a variety of animals, including marine nematodes and fish, have shown species-specific gut microbiomes, even under laboratory conditions. This, together with the frequently observed high intraspecific variability in the gut microbiome, suggests that the host genome is an important factor affecting the gut microbiome composition. In addition, the presence of closely related species may alter the composition of the gut microbiome.
We have performed a controlled experiment in which three morphologically very similar fish species have been reared together in the same tank for their whole life. In addition, the three species were also reared in separate tanks. Microbiome analysis of the gut will unveil whether bacterial composition is different between the three species. Such information is important to understand host genome-microbiome interactions which can lead to physiological adaptations and even speciation.
This internship is focused on wet lab hands-on experience in library preparation for amplicon-based next generation sequencing using Illumina technology, from DNA extraction to PCR clean-up and pooling.